Some changes in the usage of build_sigma_from_txt.

doc/guide/analysis.rst

@@ -47,15 +47,12 @@ You may also have your self energy stored in text files. For this case we provid
 :meth:`constr_Sigma_real_axis`, which loads the data and puts it into a real frequency :class:`BlockGf <pytriqs.gf.local.BlockGf>` object::
 
   from pytriqs.applications.dft.build_sigma_from_txt import *
-  SigmaReFreq = constr_Sigma_real_axis(SK, filename, hdf=False, hdf_dataset='SigmaReFreq',n_om=0, orb=0)
+  SigmaReFreq = constr_Sigma_real_axis(filename=filename, gf_struct_orb=SK.gf_struct_solver[0])
 
 where:
  
-  * `filename`: the name of the hdf5 archive file or the `fname` pattern in text files names as described above,  
-  * `hdf`: if `True`, the real axis self energy will be read from the hdf5 file, otherwise from the text files,
-  * `hdf_dataset`: the name of dataset where the self energy is stored in the hdf5 file,
-  * `orb`: index of an inequivalent shell,
-  * `n_om`: the number of points in the real-axis mesh (used only if `hdf=False`).
+  * `filename`: the `fname` pattern in text files names as described below,  
+  * `gf_struct_orb`: the Greens function structure for the regarding inequivalent shell.
 
 It is important that you follow some rules concerning the structure of your data files:
   * Each data file should contain three columns: real frequency, real part and imaginary part of the self energy exactly in this order. 

python/build_sigma_from_txt.py

@@ -10,40 +10,46 @@ def read_fortran_file (filename):
         for x in line.replace('D','E').split() :
             yield string.atof(x)
 
-def constr_Sigma_real_axis(self, filename, hdf=True, hdf_dataset='SigmaReFreq',n_om=0,orb=0, tol_mesh=1e-6):
+def line_count(fname):
+    """Counts the lines of a file"""
+    with open(fname) as f:
+        for i, l in enumerate(f):
+            pass
+    return i + 1
+        
+def constr_Sigma_real_axis(filename, gf_struct_orb, tol_mesh=1e-6):
     """Uses Data from files to construct Sigma (or GF)  on the real axis."""
 
-    if not hdf: # then read sigma from text files
-
     # first get the mesh out of any one of the files:
-        bl = self.gf_struct_solver[orb].items()[0][0] # block name
-        ol = self.gf_struct_solver[orb].items()[0][1] # list of orbital indices
+    bl = gf_struct_orb.items()[0][0] # block name
+    ol = gf_struct_orb.items()[0][1] # list of orbital indices
     if (len(ol)==1): # if blocks are of size one
         Fname = filename+'_'+bl+'.dat'
     else:
-            print 'TEST'
         Fname = filename+'_'+bl+'/'+str(ol[0])+'_'+str(ol[0])+'.dat'
 
+    try:
+        n_om = line_count(Fname)
         R = read_fortran_file(Fname)
         mesh = numpy.zeros([n_om],numpy.float_)
-        try:
+
         for i in xrange(n_om):
             mesh[i] = R.next()
             sk = R.next()
             sk = R.next()
 
     except StopIteration : # a more explicit error if the file is corrupted.
-            raise "SumkDFT.read_Sigma_ME : reading mesh failed!"
+        raise "constr_Sigma_real_axis : reading mesh failed!"
     R.close()
 
     # check whether the mesh is uniform
     bin = (mesh[n_om-1]-mesh[0])/(n_om-1)
     for i in xrange(n_om):
-            assert abs(i*bin+mesh[0]-mesh[i]) < tol_mesh, 'constr_Sigma_ME: real-axis mesh is non-uniform!'
+        assert abs(i*bin+mesh[0]-mesh[i]) < tol_mesh, 'constr_Sigma_real_axis: real-axis mesh is non-uniform!'
 
     # construct Sigma
-        a_list = [a for a,al in self.gf_struct_solver[orb].iteritems()]
-        glist = lambda : [ GfReFreq(indices = al, window=(mesh[0],mesh[n_om-1]),n_points=n_om) for a,al in self.gf_struct_solver[orb].iteritems()]
+    a_list = [a for a,al in gf_struct_orb.iteritems()]
+    glist = lambda : [ GfReFreq(indices = al, window=(mesh[0],mesh[n_om-1]),n_points=n_om) for a,al in gf_struct_orb.iteritems()]
     SigmaME = BlockGf(name_list = a_list, block_list = glist(),make_copies=False)
 
     #read Sigma
@@ -63,42 +69,9 @@ def constr_Sigma_real_axis(self, filename, hdf=True, hdf_dataset='SigmaReFreq',n
                         isig = R.next()
                         g.data[iom,iL,iR]=rsig+1j*isig
                 except StopIteration : # a more explicit error if the file is corrupted.
-                        raise "SumkDFT.read_Sigma_ME : reading Sigma from file failed!"
+                    raise "constr_Sigma_real_axis : reading Sigma from file failed!"
                 R.close()
 
-
-    else: # read sigma from hdf
-
-        omega_min=0.0
-        omega_max=0.0
-        n_om=0
-        if (mpi.is_master_node()):
-            ar = HDFArchive(filename)
-            SigmaME = ar[hdf_dataset]
-            del ar
-
-        #OTHER SOLUTION FIXME
-        #else:
-        #    SigmaME=0
-        #SigmaME = mpi.broadcast..
-
-            # we need some parameters to construct Sigma on other nodes
-            omega_min=SigmaME.mesh.omega_min
-            omega_max=SigmaME.mesh.omega_max
-            n_om=len(SigmaME.mesh)
-        omega_min=mpi.bcast(omega_min)
-        omega_max=mpi.bcast(omega_max)
-        n_om=mpi.bcast(n_om)
-        mpi.barrier()
-        # construct Sigma on other nodes
-        if (not mpi.is_master_node()):
-            a_list = [a for a,al in self.gf_struct_solver[orb].iteritems()]
-            glist = lambda : [ GfReFreq(indices = al, window=(omega_min,omega_max),n_points=n_om) for a,al in self.gf_struct_solver[orb].iteritems()]
-            SigmaME = BlockGf(name_list = a_list, block_list = glist(),make_copies=False)
-        # pass SigmaME to other nodes
-        SigmaME = mpi.bcast(SigmaME)
-        mpi.barrier()
-
     SigmaME.note='ReFreq'
 
     return SigmaME

test/sigma_from_file.py

@@ -19,7 +19,7 @@ for name, s in Sigma_hdf:
 
 # Read self energy from txt files
 SK = SumkDFTTools(hdf_file =  'SrVO3.h5', use_dft_blocks = True)
-Sigma_txt = constr_Sigma_real_axis(SK, 'Sigma', hdf=False, n_om=101, orb=0)
+Sigma_txt = constr_Sigma_real_axis(filename='Sigma', gf_struct_orb=SK.gf_struct_solver[0])
 SK.put_Sigma(Sigma_imp = [Sigma_txt])
 
 SK.hdf_file = 'sigma_from_file.output.h5'